3 research outputs found
Alterations in the epigenetic machinery associated with prostate cancer health disparities
DATA AVAILABILITY STATEMENT : Data used in this study were published by Jaratlerdsiri et al., 2022, and made accessible via the European Genome-Phenome Archive (EGA; https://ega-archive.org, accessed on 1 June 2022) under study accession EGAS00001006425 and dataset accession EGAD00001009067 (Southern African Prostate Cancer Study, SAPCS) and EGAD00001009066 (Garvan/St. Vincent’s Prostate Cancer Study).SUPPLEMENTARY MATERIALS : FIGURE S1: Optimal cluster number identification; FIGURE S2: Consensus heatmap for variant data overlapping epigenetic machinery genes based on results from ten multi-omics integrative clustering algorithms with the assigned cluster numbers of (A) k = 3 and (B) k = 8; FIGURE S3: Silhouette plot quantifying Sample Similarity based on results from ten multi-omics integrative clustering algorithms with the assigned cluster numbers of (A) k = 3 and (B) k = 8; FIGURE S4: Mutational burden in African- and European-derived tumors; FIGURE S5: Damaging variant mutational burden in African- and European-derived tumors; TABLE S1: Patient Summary or African and European Study participants; TABLE S2: SuperPaths and their associated pathways
included in this Study for their relationship to epigenetic processes; TABLE S3: List of genes assigned to Epigenetic Process Group 1 (chromatin organization and regulation); TABLE S4: List of genes assigned to Epigenetic Process Group 2 (histone modifications); TABLE S5: List of genes assigned to Epigenetic
Process Group 3 (DNA methylation); TABLE S6: List of genes assigned to Epigenetic Process Group 4 (RNA regulation); TABLE S7: List of genes assigned to Epigenetic Process Group 5 (epigenetic regulation of gene expression); TABLE S8: MOVICS clustering results; TABLE S9: Statistical Summary for tumor mutational burden (per Mb) based on all coding variants in epigenetic machinery genes in African-
and European-derived tumors; TABLE S10: Statistical Summary for tumor mutational burden (per Mb) based only on damaging variants (as per functional impact prediction) in epigenetic machinery genes in African- and European-derived tumors; TABLE S11: Independent test of epigenetic cancer Subtype
(ECS) and Small Somatic mutation to compare mutation frequency; TABLE S12: Independent test of epigenetic cancer Subtype (ECS) and Structural variation to compare Structural variation frequency; TABLE S13: Clinical Summary based on hierarchical clustering results, with epigenetic cancer Subtype
(ECS) as the grouping variable; TABLE S14: Top features, posterior probability, and rank order for joint analysis of Small Somatic mutation, Somatic Structural variant, and Somatic copy number alteration data identified by iClusterBayes; TABLE S15: Clinical Summary based on hierarchical clustering results
for Somatic copy number alteration data only, with epigenetic copy number cancer Subtype (EcnCS) as the grouping variable.African ancestry is a significant risk factor for aggressive prostate cancer (PCa), with southern African ethnicity conferring a nearly 3-fold increased global risk for associated mortality. It is well understood that epigenetic alterations drive PCa initiation and progression, coupled with somatic alterations in genes encoding epigenetic enzymes. However, differences in the somatic alterations in these genes in African- versus European-derived prostate tumors and how they may contribute to PCa health disparities has yet to be investigated, which forms the objective of this study. With current PCa care almost exclusively based on and tailored for men of European ancestry, the identification of African-specific novel PCa epigenetic cancer drivers (n = 18), including therapeutic potential (6/18), offers clinical significance with the possibility of improving healthcare approaches and health outcomes for men of African ancestry.Prostate cancer is driven by acquired genetic alterations, including those impacting the epigenetic machinery. With African ancestry as a significant risk factor for aggressive disease, we hypothesize that dysregulation among the roughly 656 epigenetic genes may contribute to prostate cancer health disparities. Investigating prostate tumor genomic data from 109 men of southern African and 56 men of European Australian ancestry, we found that African-derived tumors present with a longer tail of epigenetic driver gene candidates (72 versus 10). Biased towards African-specific drivers (63 versus 9 shared), many are novel to prostate cancer (18/63), including several putative therapeutic targets (CHD7, DPF3, POLR1B, SETD1B, UBTF, and VPS72). Through clustering of all variant types and copy number alterations, we describe two epigenetic PCa taxonomies capable of differentiating patients by ancestry and predicted clinical outcomes. We identified the top genes in African- and European-derived tumors representing a multifunctional “generic machinery”, the alteration of which may be instrumental in epigenetic dysregulation and prostate tumorigenesis. In conclusion, numerous somatic alterations in the epigenetic machinery drive prostate carcinogenesis, but African-derived tumors appear to achieve this state with greater diversity among such alterations. The greater novelty observed in African-derived tumors illustrates the significant clinical benefit to be derived from a much needed African-tailored approach to prostate cancer healthcare aimed at reducing prostate cancer health disparities.The US Congressionally Directed Medical Research Programs (CDMRP) Prostate Cancer Research Program (PCRP) Idea Development Award, the Health Equity Research Outcomes Integrity Consortium (HEROIC) Award, the National Health and Medical Research Council (NHMRC) of Australia Project Grant and Ideas Grants, a Cancer Association of South Africa (CANSA) Development Gran, the National Research Foundation of South Africa andthe Petre Foundation, Australia.https://www.mdpi.com/journal/cancershj2023School of Health Systems and Public Health (SHSPH
Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers
ADDITIONAL FILE 1: FIGURE S1. Concordant SV call generation from Manta
and GRIDSS. FIGURE S2. Summary of SVs in each type, compared to other
studies. FIGURE S3. CIRCOS plot of hyper-SV mutated tumours. FIGURE S4. The spread of SV breakpoints and samples in each 1 Mbp genomic bin. FIGURE S5. TMPRSS2-ERG fusion with interstitial region retention.
TABLE S1. Clinical and pathological characteristics of 180 prostate cancer
patients included in this study. TABLE S2. Biallelic assessment of CDK12
in hyper-duplicated samples. TABLE S3. Biallelic assessment of BRCA2 in
hyper-deleted samples.ADDITIONAL FILE 2: TABLE S4. Summary of gene fusions identified from SVs.
ADDITIONAL FILE 3: TABLE S5. SV calls resulting in gene fusions.DATA AND MATERIALS AVAILABILITY : The datasets analysed in this study were obtained and accessible through
Jaratlerdsiri et al [6], with sequence data deposited in the European GenomePhenome Archive (EGA; https://ega-archive.org) under overarching accession
EGAS00001006425 and including the Southern African Prostate Cancer Study
(SAPCS) Dataset (EGAD00001009067) and Garvan/St Vincent’s Prostate Cancer
Database (EGAD00001009066). The computational code used to analyse SV
subtypes, SV hotspots and gene fusions is available on GitHub [68].BACKGROUND : African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-
Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the
benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa
genomic studies are still biased towards small variant interrogation.
METHODS : Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis
of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four
ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity
(African versus European), with a focus on African men from southern Africa.
RESULTS : Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count)
increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation
and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived
tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion
subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate
in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion
partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV
hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic
implications for African patients.
CONCLUSIONS : In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation
for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs
in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed
ethnic disparity in advanced PCa presentation in men of African ancestry.The Medical Health and Medical Research Council (NHMRC) of Australia, University of Sydney Bridging Grant, the USA. Department of Defense (DoD) Prostate Cancer Research Program (PCRP) Idea Development.https://genomemedicine.biomedcentral.comam2023School of Health Systems and Public Health (SHSPH
African-specific molecular taxonomy of prostate cancer
Data availability
DNA-sequencing data have been deposited at the European Genome-
Phenome Archive (EGA) under overarching accession EGAS00001006425
and including the Southern African Prostate Cancer Study (SAPCS)
Dataset (EGAD00001009067 and Garvan/St Vincent’s Prostate Cancer
Database EGAD00001009066). Academic researchers meeting the
data-access policy criteria may apply for data access through the
respective data access committees. CPGEA data are available through
http://www.cpgea.com. PCAWG data are available at ICGC Data Portal
(https://dcc.icgc.org/releases/PCAWG).Prostate cancer is characterized by considerable geo-ethnic disparity. African ancestry is a significant risk factor, with mortality rates across sub-Saharan Africa of 2.7-fold higher than global averages. The contributing genetic and non-genetic factors, and associated mutational processes, are unknown. Here, through whole-genome sequencing of treatment-naive prostate cancer samples from 183 ancestrally (African versus European) and globally distinct patients, we generate a large cancer genomics resource for sub-Saharan Africa, identifying around 2 million somatic variants. Significant African-ancestry-specific findings include an elevated tumour mutational burden, increased percentage of genome alteration, a greater number of predicted damaging mutations and a higher total of mutational signatures, and the driver genes NCOA2, STK19, DDX11L1, PCAT1 and SETBP1. Examining all somatic mutational types, we describe a molecular taxonomy for prostate cancer differentiated by ancestry and defined as global mutational subtypes (GMS). By further including Chinese Asian data, we confirm that GMS-B (copy-number gain) and GMS-D (mutationally noisy) are specific to African populations, GMS-A (mutationally quiet) is universal (all ethnicities) and the African–European-restricted subtype GMS-C (copy-number losses) predicts poor clinical outcomes. In addition to the clinical benefit of including individuals of African ancestry, our GMS subtypes reveal different evolutionary trajectories and mutational processes suggesting that both common genetic and environmental factors contribute to the disparity between ethnicities. Analogous to gene–environment interaction—defined here as a different effect of an environmental surrounding in people with different ancestries or vice versa—we anticipate that GMS subtypes act as a proxy for intrinsic and extrinsic mutational processes in cancers, promoting global inclusion in landmark studies.The National Health and Medical Research Council (NHMRC) of Australia, NHMRC Ideas Grants, University of Sydney Bridging Grant, the US Department of Defense (DoD) Prostate Cancer Research Program (PCRP) Idea Development Award TARGET Africa.http://www.nature.com/natuream2023School of Health Systems and Public Health (SHSPH